[gmx-users] GROMACS Energy groups

[Justin Lemkul]

On 10/3/19 10:27 PM, Adip Jhaveri wrote:
> Hello all,
> I am simulating a system of two proteins in solution. For the simulation I
> has specified (in the .mdp file) energygrps as : Protein W_ION.
>
> Now in the output energy file, these energy groups are separated only for
> the Columbic and LJ interactions: For e.g. (Columbic : Protein-Protein),
> (Columbic Protein - W_ION). Is it possible to get a similar
> decomposition for the bonded energy terms? (Like Bond: Protein, G96Angle:
> Protein)

energygrps decompose short-range nonbonded terms, so no. The only way to 
get such terms is to make a .tpr containing only the species of interest 
and a corresponding .xtc/.trr and use mdrun -rerun to get the energies.

> Also, is it possible during post-processing to get energies for a different
> group like for each individual protein (e.g Protein_A) or would I have to
> run the simulation again with different energy groups?

Use mdrun -rerun as stated above.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================